U.S. flag

An official website of the United States government

NM_024747.6(HPS6):c.223C>T (p.Gln75Ter) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Nov 27, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV001852027.4

Allele description [Variation Report for NM_024747.6(HPS6):c.223C>T (p.Gln75Ter)]

NM_024747.6(HPS6):c.223C>T (p.Gln75Ter)

Genes:
LOC130004578:ATAC-STARR-seq lymphoblastoid silent region 2738 [Gene]
HPS6:HPS6 biogenesis of lysosomal organelles complex 2 subunit 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q24.32
Genomic location:
Preferred name:
NM_024747.6(HPS6):c.223C>T (p.Gln75Ter)
HGVS:
  • NC_000010.11:g.102065697C>T
  • NG_012029.1:g.5308C>T
  • NM_024747.6:c.223C>TMANE SELECT
  • NP_079023.2:p.Gln75Ter
  • LRG_564:g.5308C>T
  • NC_000010.10:g.103825454C>T
Protein change:
Q75*; GLN75TER
Links:
OMIM: 607522.0007; dbSNP: rs281865107
NCBI 1000 Genomes Browser:
rs281865107
Molecular consequence:
  • NM_024747.6:c.223C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002233159Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Nov 27, 2023) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Clinical and cellular characterisation of Hermansky-Pudlak syndrome type 6.

Huizing M, Pederson B, Hess RA, Griffin A, Helip-Wooley A, Westbroek W, Dorward H, O'Brien KJ, Golas G, Tsilou E, White JG, Gahl WA.

J Med Genet. 2009 Dec;46(12):803-10. doi: 10.1136/jmg.2008.065961. Epub 2009 Oct 20.

PubMed [citation]
PMID:
19843503
PMCID:
PMC3500784

Novel HPS6 mutations identified by whole-exome sequencing in two Japanese sisters with suspected ocular albinism.

Miyamichi D, Asahina M, Nakajima J, Sato M, Hosono K, Nomura T, Negishi T, Miyake N, Hotta Y, Ogata T, Matsumoto N.

J Hum Genet. 2016 Sep;61(9):839-42. doi: 10.1038/jhg.2016.56. Epub 2016 May 26.

PubMed [citation]
PMID:
27225848
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002233159.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Gln75*) in the HPS6 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 701 amino acid(s) of the HPS6 protein. This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with Hermansky-Pudlak syndrome (PMID: 19843503). ClinVar contains an entry for this variant (Variation ID: 30676). This variant disrupts a region of the HPS6 protein in which other variant(s) (p.Gln680*) have been determined to be pathogenic (PMID: 27225848). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024